1. Dave Frank & Maggie Mahan
DIFFUSION MRI
PI Dr. Kwan-Jin Jung
TA Priti Albal
Dave Frank & Maggie Mahan
12 July 2012

2. Outline Phantom Analysis Human Analysis Orientation Direction b-value
Tensor vs HARDI models
Human Analysis
Motion correction in DWI
fMRI paradigm & ROI mask creation
Tracking
Activation patterns
Crossing
Limitations

3. Disclaimer
During this presentation we will use the words “tracts” and “fibers” These refer to the trace of the principal diffusion directions We do not presume to know the physiological constructs these may or may not reflect
of which we do not assume to know the relevance to biological tracts or physiological constructs these ….

4. Phantom Analysis

5. PHANTOM Model for extra-cellular restricted diffusion
Made of interdigitating polyester yarns
1 leg = 25 bundles
1 bundle = 8800, 10 mm fibers
-the phantom is a model for extra-cellular restricted diffusion
-1 crossing phantom consisting of 2 bundles of 25 x 400 interdigitating polyester yarns equivalent to 180,000 fibers with a circular diameter of ~10m.
-Phantom cross-section is slightly elliptical with crossing angle approx 65 degrees
-1 tubular phantom length ~ 125 mm
-Solution: demineralized water, 0.5 g/l NaN3, 4 g/l NaCl
-explain how you will use the term phantom

6. DTI, b800, Direction Comparison
6 Directions
50 Directions
Tracts
216
Mean FA 0.546
Tracts
376
Mean FA
0.445
All tracts
Center ROI
Bottom left leg ROI
Tracts 58
Mean FA 0.556
Tracts
214
Mean FA
0.453
-The tensor analysis assumes that there is a single ellipsoid in each imaging voxel a single diffusion direction—as if all of the tracts traveling through a voxel traveled in exactly the same direction -all tracking parameters constant for comparisons
-[V6, 2b=0, b=800, 50slices, TR=10s, TE=100ms]
-[V50, 6b=0, b=800, 50slices, TR=10s, TE=100ms]
-Parameters:
Fiber threshold = 0.2
Step size (mm) = 1.198
Length constraint (mm): min = 30, max = 500
Max angle = 80
Smoothing = 0 Random direction
Voxelwise
Gaussian radial basis
RK4
10 million seeds
2 threads
Tracts 20
Mean FA 0.559
Tracts 72
Mean FA
0.446

7. DTI, V50, b-value Comparison
b = 800 s/mm2
b = 2000 s/mm2
Tracts
376
Mean FA
0.445
Tracts
458
Mean FA
0.408
All Tracts
Center ROI
Bottom left leg ROI
Tracts
214
Mean FA
0.453
Tracts 70
Mean FA
0.414
-tracking parameters constant
-[V50, 6b=0, b=800, 50slices, TR=10s, TE=100ms]
-[V50, 6b=0, b=2000, 50slices, TR=10s, TE=100ms]
-Parameters:
Fiber threshold = 0.13
Step size (mm) = 1.198
Length constraint (mm): min = 30, max = 500
Max angle = 80
Smoothing = 0 Random direction
Voxelwise
Gaussian radial basis
RK4
10 million seeds
2 threads
Tracts 72
Mean FA
0.446
Tracts 82
Mean FA
0.430

8. DTI/HARDI comparison (ROI placed on center crossing)
DTI, V50, b = 2000 s/mm2
HARDI, V50, b = 2000 s/mm2
In the classic diffusion ellipsoid tensor model, the information from the crossing tract just appears as noise or unexplained decreased anisotropy in a given voxel.
HARDI calculates a distribution of multiple directions in a given voxel. We just want to know which direction lines turn up the maximum anisotropic diffusion measures. If there is a single tract, there will be just two maxima pointing in opposite directions. If two tracts cross in the voxel, there will be two pairs of maxima, and so on.
HARDI resolves crossing fibers better than DTI

9. Phantom Orientation
NO MATTER HOW YOU SLICE IT, orientation to the main magnetic field makes a difference.
Best results obtained in phantoms aligned parallel to the main magnetic field.
These differences might be related to orientation-dependent susceptibilities.

10. Phantom SusceptibilityBo
-Field map shown of phantom…
-The magnetic susceptibility of the phantom leads to field inhomogeneities which interfere with the imaging gradient fields resulting in local image distortions.
-This discontinuity in susceptibility leads to two macroscopic effects in EPI: signal loss and geometric distortions.
Susceptibility artifacts occur as the result of microscopic gradients or variations in the magnetic field strength that occurs near the interfaces of substance of different magnetic susceptibility.
Large susceptibility artifacts are commonly seen surrounding ferromagnetic objects inside of diamagnetic materials (such as the human body). These gradients cause dephasing of spins and frequency shifts of the surrounding tissues. The net result are bright and dark areas with spatial distortion of surrounding anatomy. These artifacts are worst with long echo times and with gradient echo sequences.
Long readout times are sensitive to main magnetic field inhomogeneities and magnetic susceptibility. A field map can be estimated from different scans acquired at different echo times. The phase difference between the acquired images is due to the different precession frequencies, which are related to the field map via a linear relation   
Signal drop out typically occurs in gradient echo images, and thus is less of an issue for DW spin echo EPI. With respect to geometric distortion, however, field inhomogeneity behaves like a ‘background gradient’ that affects the phase of the measured signal.
The effects of susceptibility can be mitigated by combining EPI with parallel imaging to reduce the duration of the echo train and increasing the bandwidth.
The magnetic field maps which were measured at a different orientation of the phantom to the main magnetic field. Note that the field was proportional to the angle between the main magnetic field and the fiber direction.
Magnetic susceptibility is a dimensionless proportionality constant that indicates the degree of magnetization of a material in response to an applied magnetic field. If χ is positive, the material can be paramagnetic. In this case, the magnetic field in the material is strengthened by the induced magnetization. Alternatively, if χ is negative, the material is diamagnetic. As a result, the magnetic field in the material is weakened by the induced magnetization.

11. Human Analysis

12. Motion Correction in Diffusion Imaging
Registration of intensity
Rotation of the diffusion vector
Actually scanned
Starting designed
vector position
Registration
and vector rotation
Motion based on B0 images.

13. Motion Correction Procedure
Acquire diffusion-weighted (DW) images
Estimate the diffusion tensor
Simulate DW images using tensor
Motion detection by comparing the acquired and simulated DW images
First MC step: Uses measured DWI (mDWI) and B0 image mutual information as a cost function to correct motion. (discontinuity index)
This works well when mDWIs have similar intensities, but this isn’t necessarily the case.
Second MC step: Use motion corrected image to estimate tensors (simulated tensors; sD).
Third MC step: Generate simulated image by combining the sD and the B0 image.
FourthMC step: Use mDWI and simulated image mutual information as a cost function to correct motion.
This corrects for additional motion that is due to heterogeneous mDWI signal intensities, since the simulated images have the same intensity profile as the mDWIs.

14. Global Comparison No Motion Correction Motion Correction
Anterior part most affected
Metronome effect
Spatially inhomogeneous
Edges
See Evaluating_MC_vs_NOMC.doc for parameter values

15. Cingulate Comparison No MC MC Tracts = 762 Tracts = 1208
Mean FA = 0.418
Tracts = 1208
Mean FA = 0.493
MC = motion corrected
Cingulate ROI
See Evaluating_MC_vs_NOMC.doc for parameter values

16. fMRI Paradigm
Interested in using dorsolateral prefrontal cortex as a mask in tracking analysis
DLPFC elicited by memory encoding (cue) 2s 8s
Probe
Cue
Rest 18s
Retention
face working memory task created in ePrime
a block of the task is shown
this block was repeated 10 times with 10s fixation in the beginning and end of the run

17. Group Activation for Cue
ROI: Dorsolateral Prefrontal Cortex R L z8

18. 2 Patterns of Activation
Participant 1
Participant 2

19. Crossing Fibers (HARDI, 128 Directions, b2000) Participant 1

20. Crossing Problem

21. Ventral-Rostral Fiber Redirection

22. Due to Rostral U-Fibers?

23. Take Home Messages Diffusion imaging dependent on:
ROI, b-value, # of directions, & orientation
Diffusion imaging particularly susceptible to subject motion
Subject comparisons in diffusion imaging not trivial
Tracking is a useful exploratory technique